piRNA Browser Manual
What is the piRNA Browser?
piRNA browser helps you to search any DNA motif within 100nt of any annotated piRNA. It marks found motifs as well as other piRNAs in close proximity, in addition to showing each motifs position. You can also get union or intersection of multiple motifs at the same time, making it as a nice CRISPR tool, too.
How it works ?
It was designed to work off-campus, so, just double-click the html file, and it works! Please be sure that you have a working internet connection. All sequence information is embedded in the html file. If you have new sequences to be added, please contact Burak (Burak.Ozgoren@umassmed.edu).
Sections of the tool and the search options
1. Search piRNA by name : Enter piRNA alias to search ( e.g.: 21ur-3)
2. Get : When you click ‘Get’ button, it will display only given piRNA with searched motifs, if any.
3. Reset : It resets the search by piRNA
4. Search piRNA region by motif : Enter DNA motif to search. You can also use Regular Expressions for advanced search, see the table below.
5. Search : When you click ‘Search’ button, it will return all piRNAs having the motif
6. Help : This Manual
7. Options :
7.1. Upstream : It searches for the given motif only in upstream of sequences, up to the given number of nucleotides from the first nucleotide of piRNAs.
7.2. Downstream : It searches for the given motif only in downstream of sequences, up to the given number of nucleotides from the last nucleotide of piRNAs.
7.3. piRNA : It searches for the given motif only in piRNA sequence.
7.4. Interval : It searches for the given motif between given positions, 0 being the first nucleotide of a piRNA, -1 to -100 being upstream, 21 to 121 being downstream.
8. Contain all motifs : It displays piRNA sequences having either union or intersection of given motifs.
9. Sorting
9.1. IP-input-CHR : Sort by either IP or input ppm values, or chromosome location.
9.2. 200 : Number of result to display. Start with lower numbers first in order to be sure that your browser does not crash.
10. Motifs: All searched motifs
11. List of piRNAs containing searched motifs
piRNA browser helps you to search any DNA motif within 100nt of any annotated piRNA. It marks found motifs as well as other piRNAs in close proximity, in addition to showing each motifs position. You can also get union or intersection of multiple motifs at the same time, making it as a nice CRISPR tool, too.
How it works ?
It was designed to work off-campus, so, just double-click the html file, and it works! Please be sure that you have a working internet connection. All sequence information is embedded in the html file. If you have new sequences to be added, please contact Burak (Burak.Ozgoren@umassmed.edu).
Sections of the tool and the search options
1. Search piRNA by name : Enter piRNA alias to search ( e.g.: 21ur-3)
2. Get : When you click ‘Get’ button, it will display only given piRNA with searched motifs, if any.
3. Reset : It resets the search by piRNA
4. Search piRNA region by motif : Enter DNA motif to search. You can also use Regular Expressions for advanced search, see the table below.
5. Search : When you click ‘Search’ button, it will return all piRNAs having the motif
6. Help : This Manual
7. Options :
7.1. Upstream : It searches for the given motif only in upstream of sequences, up to the given number of nucleotides from the first nucleotide of piRNAs.
7.2. Downstream : It searches for the given motif only in downstream of sequences, up to the given number of nucleotides from the last nucleotide of piRNAs.
7.3. piRNA : It searches for the given motif only in piRNA sequence.
7.4. Interval : It searches for the given motif between given positions, 0 being the first nucleotide of a piRNA, -1 to -100 being upstream, 21 to 121 being downstream.
8. Contain all motifs : It displays piRNA sequences having either union or intersection of given motifs.
9. Sorting
9.1. IP-input-CHR : Sort by either IP or input ppm values, or chromosome location.
9.2. 200 : Number of result to display. Start with lower numbers first in order to be sure that your browser does not crash.
10. Motifs: All searched motifs
11. List of piRNAs containing searched motifs